Thread by @PeacockFlu

Lots of reports of Omicron sequences carrying Delta-like mutations (eg P681R or L452R). Although a subset of these might end up being real, the vast majority will most likely turn out to be contamination or coinfection. No clear signals of anything real or nasty happening (yet).

To be sure a signal like this is real you really want multiple sequencing labs finding the same recombinant/homoplasy independently (or at least on different sequencing runs) - ideally you would look into the raw seq files as well and show no mixed bases.

As far as I understand it these are appearing now for two reasons:
1) Lots of Delta and Omicron circulating in the same areas
2) Some older sequencing primer sets being less effective at picking up parts of Omicron so low level contamination with Delta being selectively picked up

Finally its worth adding... much of what we understand about what makes Delta more transmissible/infectious, Omicron already possess - its currently unclear to me what Omicron could have to gain from Delta (with what we currently know at least)

Just to add to this thread as there's further similar reports... True recombinants don't tend to appear until a few weeks/months after there's been substancial co-circulation - we're only a couple of weeks into Omicron - I really doubt there are any prevelent recombinants yet...

Small update: the Cypriot 'Deltacron' sequences reported by several large media outlets look to be quite clearly contamination - they do not cluster on a phylogenetic tree and have a whole Artic primer sequencing amplicon of Omicron in an otherwise Delta backbone.

Here's a short thread with the evidence this is likely not real below (because I apparently can't thread properly):

https://twitter.com/PeacockFlu/status/1480210615004246027